Now, this is great news for those of us who care about all things open – open access, “open science”, open data; and people who follow developments in web technology. However, we need to make it relevant and accessible to the people who matter: interested research scientists with the question “how can I make my data more accessible”. Those people are unlikely to subscribe to the W3C mailing list. So rise up blogging community – start writing short, clear informative posts in non-specialist language, aimed at explaining to a bench scientist why they should care and what they should know concerning this protocol.

John Hawks has had a busy week following his major publication on accelerated evolution. He writes:

What I most want to point out is that the discussion on blogs is at a very high level — people are reading the paper with much more precision than I have ever experienced in the peer review process

If I could have one wish come true in 2008, it would be for more scientists in academia to realise that so-called “non-traditional” modes of publishing, debate and communication are of equal value (for me personally, higher value) to the old ways that they insist on defending, regardless of the evident flaws in those ways.

People are finding many outlets for their work. Pierre maintains a repository of tools where you can find IBDStatus, his latest software for genetic analysis.

Spotted in Nature this week:

Makes perfect sense doesn’t it: if you publish an article on a structure, include a link to the PDB resource. Yet so far as I can tell this is a new feature, since it jumped out at me. Given that the WWW is such a rich publishing platform, simply because of hyperlinks that connect data, how long before paper copies of all journals are considered quaint and obsolete?

Without realising it I’ve become a big user of Google Docs, mostly by importing from GMail attachments. On rare occasions I find the 500 KB maximum file size to be a problem – I’d suggest 1 MB is a more sensible maximum – but it does encourage people to keep embedded content out of their text documents.

On the topic of word processor alternatives, AbiWord has come a long way and now boasts a seriously-useful plugin list.

Pedro has started an open science project to study domain family expansion. He’s trialling Google Code as his project repository. I think this is a great idea and a very exciting approach. If you have anything to contribute, go and check it out. While you’re there, click the bioinformatics tag to see another 54 projects at Google Code. Quite a resource, although a few are not very active.

And in open science synchronicity, David Ng publicises Rosie Redfield’s lab on BoingBoing and links to his blog post where she discusses the benefits of open science and blogging. The few comments so far focus on the old “but won’t we get scooped” argument, so head over there and say something positive.

We must keep pushing the agenda – open research will be the norm one day, I’m sure of it.

I like the concept of workflows – really, I do – and I understand that they are used widely in industry: biotech, pharma, drug design and so on. But I predict that they will never find wide application in academic biological sciences research. Why? Because in my experience it’s essentially impossible to convince biologists that things like standards, file formats, appropriate software tools, clean code and logical organisation of computational data are important. Let me give you a typical example of a “bioinformatics problem” in academia:

Dear Neil,
Here are the sequences that you asked for. They are in fasta format, except that I’ve marked the acetylation sites with a “*” and after that, a score in square brackets.

Glancing through my November archive, I note (1) few if any bioinformatics posts and (2) few posts of any kind. Well, sometimes blogging has to take a back seat. It seems many of us are snowed under in the run-up to the holidays.